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- PDB-6fu9: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -

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Basic information

Entry
Database: PDB / ID: 6fu9
TitleComplex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with the HMA domain of Pikm-1 from rice (Oryza sativa)
Components
  • AVR-Pik protein
  • NBS-LRR class disease resistance protein
KeywordsANTIFUNGAL PROTEIN / Plant NLR / fungal effector / Plant immunity / Complex
Function / homology
Function and homology information


response to other organism / ADP binding / defense response / ATP binding / metal ion binding
Similarity search - Function
Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / NB-ARC / NB-ARC domain / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Disease resistance protein Pikm1-TS / AVR-Pik protein
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
Magnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsFranceschetti, M. / De la Concepcion, J.C. / Banfield, M.J.
Funding support United Kingdom, Japan, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J00453 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P012574 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M02198X United Kingdom
European Research Council743165
Japan Society for the Promotion of ScienceKAKENHI 15H05779 Japan
CitationJournal: Nat Plants / Year: 2018
Title: Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen.
Authors: De la Concepcion, J.C. / Franceschetti, M. / Maqbool, A. / Saitoh, H. / Terauchi, R. / Kamoun, S. / Banfield, M.J.
History
DepositionFeb 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NBS-LRR class disease resistance protein
B: AVR-Pik protein
C: NBS-LRR class disease resistance protein
D: AVR-Pik protein


Theoretical massNumber of molelcules
Total (without water)38,7514
Polymers38,7514
Non-polymers00
Water5,188288
1
A: NBS-LRR class disease resistance protein
B: AVR-Pik protein


Theoretical massNumber of molelcules
Total (without water)19,3752
Polymers19,3752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-2 kcal/mol
Surface area8410 Å2
MethodPISA
2
C: NBS-LRR class disease resistance protein
D: AVR-Pik protein


Theoretical massNumber of molelcules
Total (without water)19,3752
Polymers19,3752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-5 kcal/mol
Surface area9020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.090, 87.130, 103.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NBS-LRR class disease resistance protein


Mass: 8547.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Pikm1-TS, Pi-km1 / Production host: Escherichia coli DH1 (bacteria) / References: UniProt: B5UBC1
#2: Protein AVR-Pik protein / AVR-Pik protein ( Pikmprotein / Pikp protein ) / AvrPi7 protein


Mass: 10827.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: AVR-Pik, AvrPik, Pikm, Pikp / Production host: Escherichia coli DH1 (bacteria) / References: UniProt: C4B8B8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.12M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene-glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol); 0.1M Buffer system 3 (1M Tris (base); BICINE) pH 8.5; 50% v/v ...Details: 0.12M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene-glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol); 0.1M Buffer system 3 (1M Tris (base); BICINE) pH 8.5; 50% v/v Precipitant mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9168 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9168 Å / Relative weight: 1
ReflectionResolution: 1.2→29.04 Å / Num. obs: 104301 / % possible obs: 98.5 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 21.7
Reflection shellResolution: 1.2→1.23 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia20.4.0.0data reduction
Aimless0.5.17data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A6W

5a6w


Resolution: 1.2→29.04 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.588 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.039 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18435 5033 4.8 %RANDOM
Rwork0.14852 ---
obs0.15025 99199 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å20 Å2
2---0.78 Å20 Å2
3---2.13 Å2
Refinement stepCycle: 1 / Resolution: 1.2→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2573 0 0 288 2861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192702
X-RAY DIFFRACTIONr_bond_other_d0.0020.022557
X-RAY DIFFRACTIONr_angle_refined_deg1.9021.9553666
X-RAY DIFFRACTIONr_angle_other_deg1.11235963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4735348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92124.017117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50115484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8071517
X-RAY DIFFRACTIONr_chiral_restr0.1230.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213008
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02549
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3262.0091336
X-RAY DIFFRACTIONr_mcbond_other3.3272.0071335
X-RAY DIFFRACTIONr_mcangle_it4.3233.0241669
X-RAY DIFFRACTIONr_mcangle_other4.3223.0251670
X-RAY DIFFRACTIONr_scbond_it3.6192.3261366
X-RAY DIFFRACTIONr_scbond_other3.622.3251366
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2533.3471985
X-RAY DIFFRACTIONr_long_range_B_refined5.68524.7372965
X-RAY DIFFRACTIONr_long_range_B_other5.61424.3512915
X-RAY DIFFRACTIONr_rigid_bond_restr3.75235259
X-RAY DIFFRACTIONr_sphericity_free30.7545204
X-RAY DIFFRACTIONr_sphericity_bonded16.53955272
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 308 -
Rwork0.258 6450 -
obs--87.58 %

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